This project focuses on the human Y chromosome in the context of the Human Genome Project. The principal long-term goal of this project is complete definition of the genetic content of the human Y chromosome. The present four-year proposal has two components: Mapping. The Y chromosome, like some other regions of the human genome, is inherently difficult to map (and sequence) because of a high concentration of chromosome-specific repetitive sequences. The investigators aim to develop robust methods for STS generation and physical mapping in regions of the genome that are rich in chromosome-specific repetitive sequences. They will apply these methods in constructing, for the Y chromosome's 30-Mb euchromatic region, a highly integrated physical map, the focal point of which will be a set of minimally overlapping, fidelity-verified BAC clones suitable for efficient and systematic sequencing. This integrated map will also include 1200 STSs (at an average spacing of 25 kb), a radiation hybrid map, and a refined deletion map based on naturally occurring deletions as found in human individuals. Sequencing. The investigators aim to initiate large-scale sequencing of the euchromatic region in collaboration with the NCHGR-funded Sequencing Group at the Whitehead/MIT Center for Genome Research. The concentration of repetitive sequences makes the Y chromosome, like some other regions of the human genome, an inherently difficult sequencing target. The investigators aim to develop robust, cost-effective solutions for sequence assembly and sequence finishing problems that plague repeat-rich regions of the genome, and to collaborate with the Sequencing Group in determining the nucleotide sequence of one quarter of the Y chromosome's euchromatic region (7.5 Mb). The resulting map and sequence information will provide a framework for elucidating the function of the Y chromosome in medically relevant processes as diverse as spermatogenesis, tumorigenesis, and embryonic development.